Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures
Abstract Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and...
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Springer Nature
2017-02-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20167159 |
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| author | Nicholas A Graham Aspram Minasyan Anastasia Lomova Ashley Cass Nikolas G Balanis Michael Friedman Shawna Chan Sophie Zhao Adrian Delgado James Go Lillie Beck Christian Hurtz Carina Ng Rong Qiao Johanna ten Hoeve Nicolaos Palaskas Hong Wu Markus Müschen Asha S Multani Elisa Port Steven M Larson Nikolaus Schultz Daniel Braas Heather R Christofk Ingo K Mellinghoff Thomas G Graeber |
| author_facet | Nicholas A Graham Aspram Minasyan Anastasia Lomova Ashley Cass Nikolas G Balanis Michael Friedman Shawna Chan Sophie Zhao Adrian Delgado James Go Lillie Beck Christian Hurtz Carina Ng Rong Qiao Johanna ten Hoeve Nicolaos Palaskas Hong Wu Markus Müschen Asha S Multani Elisa Port Steven M Larson Nikolaus Schultz Daniel Braas Heather R Christofk Ingo K Mellinghoff Thomas G Graeber |
| author_sort | Nicholas A Graham |
| collection | DOAJ |
| description | Abstract Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan‐cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis‐defined CNA signatures are predictive of glycolytic phenotypes, including 18F‐fluorodeoxy‐glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer‐linked metabolic enzymes. A pan‐cancer and cross‐species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer‐driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution. |
| format | Article |
| id | doaj-art-ecca9cc2cad345a0a0b562644ca81d88 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2017-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-ecca9cc2cad345a0a0b562644ca81d882025-08-20T04:03:12ZengSpringer NatureMolecular Systems Biology1744-42922017-02-0113212510.15252/msb.20167159Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressuresNicholas A Graham0Aspram Minasyan1Anastasia Lomova2Ashley Cass3Nikolas G Balanis4Michael Friedman5Shawna Chan6Sophie Zhao7Adrian Delgado8James Go9Lillie Beck10Christian Hurtz11Carina Ng12Rong Qiao13Johanna ten Hoeve14Nicolaos Palaskas15Hong Wu16Markus Müschen17Asha S Multani18Elisa Port19Steven M Larson20Nikolaus Schultz21Daniel Braas22Heather R Christofk23Ingo K Mellinghoff24Thomas G Graeber25Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaDepartment of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of CaliforniaDepartment of Laboratory Medicine, University of CaliforniaDepartment of Genetics, M. D. Anderson Cancer Center, The University of TexasDepartment of Surgery, Icahn School of Medicine at Mount SinaiDepartment of Radiology, Memorial Sloan Kettering Cancer CenterMarie‐Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer CenterCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaDepartment of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of CaliforniaHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer CenterCrump Institute for Molecular Imaging, David Geffen School of Medicine, University of CaliforniaAbstract Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan‐cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis‐defined CNA signatures are predictive of glycolytic phenotypes, including 18F‐fluorodeoxy‐glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer‐linked metabolic enzymes. A pan‐cancer and cross‐species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer‐driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution.https://doi.org/10.15252/msb.20167159aneuploidyDNA copy number alterationsgenomic instabilityglycolysismetabolism |
| spellingShingle | Nicholas A Graham Aspram Minasyan Anastasia Lomova Ashley Cass Nikolas G Balanis Michael Friedman Shawna Chan Sophie Zhao Adrian Delgado James Go Lillie Beck Christian Hurtz Carina Ng Rong Qiao Johanna ten Hoeve Nicolaos Palaskas Hong Wu Markus Müschen Asha S Multani Elisa Port Steven M Larson Nikolaus Schultz Daniel Braas Heather R Christofk Ingo K Mellinghoff Thomas G Graeber Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures Molecular Systems Biology aneuploidy DNA copy number alterations genomic instability glycolysis metabolism |
| title | Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures |
| title_full | Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures |
| title_fullStr | Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures |
| title_full_unstemmed | Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures |
| title_short | Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures |
| title_sort | recurrent patterns of dna copy number alterations in tumors reflect metabolic selection pressures |
| topic | aneuploidy DNA copy number alterations genomic instability glycolysis metabolism |
| url | https://doi.org/10.15252/msb.20167159 |
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